An Alternate Choice
by iRiDeScEnT DrReAm
Summary: "My brother, Jonathan Morgenstern. Can you bring him back and erase the evil in him? Make him a good person again?" On that night in City of Glass, Jace never dies and Clary asks the Angel to bring back Jonathan instead. But in the Shadow World, there are always consequences...
1. Prologue

_After I read City of Heavenly Fire, I cried so hard when Jonathan died. I swear, it was like the saddest thing ever. _

_And then this idea popped into my head. _

_What if Valentine hadn't killed Jace? If Jace had been alive and never gone to Lake Lyn after passing out from his fight with Sebastian? What else could Clary have wished for? _

_Happy reading! _

_Disclaimer: I do not own the Mortal Instruments._

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><p><strong>Prologue<strong>

_"__The Battle on Brocelind Plain is ending. Morgenstern's hold over his demons vanished with his death. Already many are fleeing; the rest will soon be destroyed. There are Nephilim riding to the shores of this lake at this very moment. If you have a request, Shadowhunter, speak it now." The Angel paused. "And remember that I am not a genie. Choose your desire wisely." _

_Clary hesitated, only for a moment but the moment stretched out as long as any moment ever had. She could ask for anything, she thought dizzily, anything-an end to pain or world hunger or disease, or for peace on earth. But then again, perhaps these things weren't in the power of angels to grant, or they would already have been granted. And perhaps people were supposed to find these things for themselves. _

- _Pages 452-453, City of Glass_

Suddenly, something else came to mind. A picture of her mother, sitting on her bed, crying over a lock of blonde hair. Her brother's hair. Crying over the son she should have had.

And then Clary knew what she wanted.

But before that, she had one last thing she needed to know.

"Jace," she said, a little breathlessly. "Jonathan Herondale. Is he alright?"

Raziel sounded impatient now. _Jonathan Herondale is unconscious, but he has been found and his wounds are being treated as we speak. He will be fine._

Her decision was made.

Clary raised her eyes to meet the Angel's. "My brother, Jonathan Morgenstern. Can you erase the evil in him? Make him a good person again?"

The Angel said nothing for a minute, simply looking down at Clary, his face impassive. Clary experienced a moment of panic - did Raziel intend to grant her wish at all? Would he simply strike her down, like he had struck down Valentine?

_Close your eyes, Clarissa Morgenstern. _

Obediently, Clary closed her eyes; you didn't say no to an angel, no matter how apprehensive you might be. An image came to her head, unbidden, of a boy with blonde hair and spring green eyes, a boy who could love and laugh and be human. She kept the image in her head, replacing the fake smirk with a genuine smile, the fathomless dark eyes with twinkling green ones. _My brother. _

"Clary?"

She opened her eyes immediately, the voice invoking memories of the boy she had known only as Sebastian. The first thing she registered was that Raziel was gone, the night sky seemed darker than usual with the blinding white light of the halo that had surrounded him.

The second was that there was a boy kneeling next to her, his expression concerned. His white blonde hair fell into his green eyes - the exact same colour of hers.

"Jonathan?" she whispered, hardly able to believe that Raziel had actually done it; had managed to burn away the demon blood and make him a true Shadowhunter instead.

"Clary," he said, just as quietly. They stared at each other in astonishment, drinking in every detail about each other. "You really are Jonathan?" she asked, still thinking she was dreaming. "Not Sebastian?"

He nodded, and a genuine smile transformed his features. "I'm Jonathan. I have no more demon blood in me."

Clary looked at him, and she _knew. _She felt again the feeling of familiarity she had experienced at the Penhallows' house, but stronger - as if her subconscious had realized that this was really her brother, someone who could protect her and care for her and love her. She felt tears rolling down her cheeks, and Jonathan gently wiped them away.

She felt herself half-laughing, half-sobbing as a crushing sense of relief overtook her. Everything was finally alright.

It was over.


	2. Chapter 1

_6 reviews and 10 favourites already! _

_I'm so glad to see that you guys like Jonathan too, and I'm not the only one who was upset about the end of City of Heavenly Fire. This was originally going to be in the prologue, but I decided to make it into another chapter instead because it was too long. _

_There will be a bit of drama in this one, as well as Jonathan-Clary sibling bonding! :) I know you're all dying for that. _

_Happy reading! _

_Disclaimer: I do not own The Mortal Instruments._

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><p><em>"I'm wide awake. And now it's clear to me that everything you see, ain't always what it seems. I'm wide awake, and I was dreaming for so long. I wish I knew then what I know now, wouldn't dive in, wouldn't bow down. Gravity hurts and you made it so sweet. Till I woke up on, on the concrete. Falling from cloud nine, crashing from the high...I'm letting go tonight. Yeah, I'm falling from cloud nine..."<em>

_- Wide Awake, Katy Perry_

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><p><strong>Chapter One<strong>

Clary was exhausted.

It was three in the morning and she had just finished repeating her story about ten times: to Jia Penhallow, to Jocelyn, to Luke, to Simon and Isabelle and Jace.

To put it plainly, she felt she had done quite enough talking for the day.

Jonathan had stayed silent. Clary couldn't really blame him; the suspicious looks and whispers sent his way didn't make anything easier. Clary could almost imagine what the Shadowhunters must be saying about them. _Mad. Untrustworthy. Valentine's children…_

Not for the first time, she felt a surge of hatred against Valentine. It hadn't been enough for him to torture them all when he was alive; even when he was dead, he still cast his shadow upon his children, tarnishing their name and reputation.

Clary's eyes lingered on the doorway which Isabelle had dashed through not so long ago, taking Simon with her. Clary had had to beg Simon and Jace to physically restrain her until she explained the full story to them.

Isabelle had stayed silent throughout the tale, only to leave immediately when it was over. Shooting Clary an apologetic look, Simon had followed after her.

Clary knew that someone should have gone after Isabelle-who knew what she would do in this frame of mind-but she still fervently wished Simon was there to talk to her, to help her figure it all out.

Jonathan was standing next to her, his arms crossed firmly across his chest. His green eyes were worried, and she could tell from the way his fists were clenched that he was tense. She marvelled that how, just a day ago, the same boy she had called enemy was now someone she thought she could love.

Because she didn't love Jonathan-not just yet-but she cared about him. It had barely been a few hours since she had gotten her brother back but already she felt a protectiveness towards him, a feeling that made her want to defend him against all the unjust barbs and accusations being flung in his direction.

She didn't know if he felt that way about her, but she thought he did; he constantly glanced at her as if to reassure himself that she was still there, and there was a quiet concern in his eyes and expression.

Another person who couldn't keep her eyes off the two of them was Jocelyn.

In all honesty, Clary had been expecting some dramatic reaction; for Jocelyn to faint, or cry or at least _say something_. Instead her mother had gone pale white and demanded to know what had happened on the shores of Lake Lyn; after pulling Clary into a fierce bear hug and scolding her furiously for going off on her own.

Now it seemed all she could do was stare at her son, as if she was drinking him in.

"Clary, can I talk to you?"

Startled, it took Clary a few seconds to realize that it was Jonathan who was talking to her. Nodding her assent, she turned to follow him out into the hallway-and found her path blocked by Jace. Not for the first time, she marvelled at how he could move so fast; he had been at the opposite end of the room just a second ago.

"Jace, I appreciate the fact that you finally want to talk to me, but now is not the time. Move."

"Clary, you're not going anywhere with him," Jace said in a quiet but firm voice. He shot a cool glance to where Jonathan waited just outside the room.

Clary's temper, already stretched thin with all the murmurs she could hear in the Accords Hall, snapped. "And who do you think you are to order me around like that? I'll do whatever I want!"

Jace was unfazed. "I don't care what you want. You're not going anywhere alone with him. I'm not going to trust him just yet, good or not."

"HE ISN'T SEBASTIAN!" Clary finally yelled, getting tired of all the suspicious looks and hard stares she had endured. "He's Jonathan, he's a person who never got to live and now when he finally has a chance to, you treat him like this! I asked Raziel to remove the demon blood from him! Or is that you don't trust that Raziel did what I asked of him?"

This broke Jace's composure. "Clary-"

"Don't you _Clary _me!" she snapped. "I'm going to have a moment with my brother, and while we're on the topic of Sebastian, do you want to tell me why you went chasing off after him? How you blatantly _lied _to me and went off on some goddamn suicide mission?"

Jace's eyes held a hint of guilt and regret but before he could say anything Clary stomped past him and slammed the door in his face.

She had had _enough. _

Breathing hard, she looked up, noticing how Jonathan's gaze held a calm and final look. "Why did you do that?" he asked her. "Do what?" Clary shot back, confused.

"Defend me."

She stared. "Because-because you're my brother, and everyone still thinks you're Sebastian without even giving you a chance. How is that fair?"

"They're right not to trust me, Clary," Jonathan returned. "I've betrayed the trust of so many people, destroyed the lives of so many more, and nearly annihilated Shadowhunters forever. How can they possibly trust-?"

"Because they don't trust _me_!" Clary retorted. "I told them about Raziel, I endured all their trials, didn't object to holding the Soul-Sword-isn't that good enough? Or they do they somehow think I managed to lie holding the sword as well?"

She wished, desperately, that there was some rune to show them what had happened, some rune she could use to tell them that she wasn't lying, that Raziel had really-

It happened.

A spiralling network of swirls and lines exploded in her mind, forming a rune that she couldn't really describe; but the name came to her clearly. _Denarro Praeterita. Show the past. _

Ignoring the puzzled "Clary?" uttered by Jonathan, Clary sprinted to the end of the hallway and out the door, emerging in the middle of the Accords Hall-when the full Clave was in session.

She came to a halt in the centre of the hall, ignoring the vehement exclamations and hostile gazes fixated upon her. Instead she knelt upon the floor and, with her stele clutched firmly in her hand, began to draw.

The rune took shape, spreading along the floor as the sizzling black lines burned from the tip of her stele. When Clary was finished, she stood back, letting the whole Clave see what she had done.

The lines started to blur together, blending into one big black mess that suddenly seemed to sink right _into _the floor and spread in a one big line around it, forming a square.

In the centre of the square, an image appeared.

And Clary breathed a sigh of relief. It had worked.

She moved away, letting the rune tell the story much better than she herself ever could have, the shocked expressions and stifled gasps the only background noise.

Finally, it came to an end, and this time there was a pin-drop silence. Clary spotted Maryse and Robert Lightwood among the Nephilim. Clary thought Maryse's expression held a hint of pride. Noticing her gaze, Maryse nodded stiffly, and Clary felt astonished. She had always known Maryse didn't really like her but maybe now she had gained the woman's respect.

Robert Lightwood's expression was perfectly calm and placid. "You may go, Clarissa. Thank you for showing us that."

Hardly believing that she had actually done it, Clary slipped out of the hall and closed the door behind her.

Only to find both Jonathan and Jace waiting for her. Standing right next to each other, Clary couldn't help but notice how they looked so similar to each other-both of them were the same height and with their golden hair and complexion, they might as well have been brothers.

_They were, _Clary realized bemusedly. Not by blood, but Valentine had raised both of them with the same iron fist and she could see it in everything; in the fluid grace with which they moved, the way they held themselves, even in the way their blonde hair fell into their eyes.

They even had the same first name: Jonathan Herondale and Jonathan Morgenstern.

"What was that about?" Jace demanded, taking a step forward. "Did the Clave come to a decision?"

"No," Clary sighed. "They're still deliberating." Suddenly, she scowled. "And don't think you're getting off easy. You still have to answer to me about Sebastian."

At this, she noticed Jonathan flinch and felt a stab of guilt. Pushing it away, she glared at Jace, folding her arms over her chest. Clary admitted to herself that there was no way in hell she could look intimidating and this proved to be true when Jace chuckled and Jonathan cracked a smile.

"This is Clary as you will come to know and love," Jace announced to Jonathan. "First lesson to learn: she never lets anything slip by her so be careful what you do and say."

"Got it," Jonathan noted, nodding his head seriously.

Clary narrowed her eyes. "Since when did you two get all buddy-buddy? Last I saw, it was all 'you're not spending any time with him!'"

Jace shrugged. "I saw what you did in there," he gestured to the door. "And I thought I'd…give him the benefit of the doubt, say."

Clary's tense posture relaxed. "Good. Now can I please talk to him alone?"

Jace looked from Clary to Jonathan, nodded tersely, and went back into the room. Clary craned her head back to look into Jonathan's eyes as he approached. _Figures, _she groaned internally. _He'd probably get all the good genes, too. _

"Clary," Jonathan started off, staring at a spot over her head. "I…thank you."

Clary was taken aback. "Why?"

"I thought Jace wouldn't tell you this part," Jonathan smiled wryly. "He killed me-Sebastian that is."

"He did _what_?" Clary gasped. "But you were-Sebastian had demon blood! He was invincible!"

Jonathan nodded. "Isabelle helped him. He managed to kill Sebastian when he was distracted with Isabelle. Stabbed him through the heart."

"So…Raziel not only ridded you of the evil, but he also brought you back from the dead?" Clary questioned.

"Yes." Jonathan hesitated. "And….I wanted to say that I'm sorry. I know that I'm not Sebastian but it still remains that it was me who did all of those things. And I know there'll always be those who won't trust me because of that. But please, believe me Clary. I'll never forget what I did till the day I die. I'll regret it for the rest of my life."

"I believe you," Clary said quietly. "But I know you're a good person. And I will always believe that."

Jonathan was looking down at his feet now. "And, I'm also sorry for kissing you by the Fairchild manor the other day."

Clary was very sure her cheeks had gone fire-engine red.

"That's…fine," she stammered. "But I think we probably shouldn't tell that to Mom. She'd probably freak…since it's sort of, um, incest and all. Even though it was Sebastian, not you."

"By the Angel, Sebastian was an asshole," Jonathan looked up, emerald eyes bright with hatred.

"That he was," agreed Clary fervently.

They stood there looking at each other, siblings united after sixteen years of being apart. She knew that she had only come to know Jonathan a few hours ago but he felt as familiar to her as Luke. He wasn't a stranger; he was someone whose blood flowed in her veins too, someone who she would irrevocably love and care for one day and be loved and cared for in return.

On a whim, she stepped forward and hugged him.

She felt him tense and stiffen for a minute before he gingerly wrapped his arms around her and pulled her closer to him. "I've never been hugged before," he murmured into her hair. "Valentine wasn't one for coddling me. _To love is to destroy_."

Clary hugged him harder, her heart going out to her brother. To not receive any love and affection for eighteen years…she couldn't ever imagine not being kissed or hugged by her mother. "Forget about him," she murmured into his shirt. "You're free of him now."

Finally.

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><p><em>Yes, the ending was cliché and lame and too mushy. But you know what, I don't care because I got my Jonathan and Clary bonding moment! And I know Clary, Jace and Jonathan are a bit OOC in this but please bear with me. Like I said before, this is my first Mortal Instruments fanfic and I do need time to get adjusted to writing the characters. <em>

_Please review, since I spent my time writing this chapter for you instead of studying like I was supposed to….so make it worthwhile! _

_Till next time! _


	3. Chapter 2

_Hey guys! Thanks for the reviews, great to know you didn't think it was too mushy or cliché. _

_In this chapter we have some Jace/Jonathan bonding and some Jocelyn/Jonathan bonding as well. I love seeing Jonathan bond with people – maybe I'm just crazy. _

_Happy reading! _

_Disclaimer: I do not own the Mortal Instruments._

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><p><em>"<em>_All your insecurities, all that dirty laundry. Never made me blink one time. Unconditional…unconditionally. I will love you, unconditionally. There is no fear now, let go and just be free. I will love you, unconditionally…" _

- _Unconditionally, Katy Perry_

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><p><strong>Chapter Two <strong>

Being stuck in a room with someone who you had killed barely twelve hours ago was not exactly an ideal situation.

For the first time in his life, his smooth-talking skills were failing him and Jace did not like it one bit.

Both boys were leaning on walls opposite each other and Jace was taking the time to surreptitiously observe Clary's brother – Jonathan was his brother too, he supposed. After all, they had both been raised by Valentine.

"You can just say it, you know," Jonathan broke the silence, his voice dry. "I know you hate me."

Jace raised an eyebrow. "What makes you say that?"

Jonathan laughed – but it was wry, bitter laugh. "Doesn't everyone?" he asked. "Valentine's son – took the wards down – traitor, murderer, enemy…"

He trailed off, eyes fixed on the door that Clary had vanished through a few minutes ago.

Jace hadn't known what exactly had transpired between the siblings in the hallway but he had noticed a difference. He hadn't wanted to ask; he got the feeling it was a private brother-sister bonding moment.

Jace didn't often feel sorry for people but looking at the boy across from him, he felt a tinge of empathy. He knew what it was like to ostracized because of who your parents were; he had experienced it in those few terrible weeks he thought he was Valentine's son. People who had previously trusted him now became more wary; the Inquisitor had held a grudge against him where she had had none before; Maryse herself had kicked him out of the Institute, even if it was for a brief time.

The injustice still rankled within him.

"I don't hate you," Jace finally found his voice. "I hate Sebastian. I don't know you, so how could I hate you?"

Jonathan looked up. "But I know about you. Valentine told me about you all the time."

"Well, he had to play the proud parent I suppose."

Jonathan cracked a real smile. "Him?"

"Not likely, then?"

"No."

"Well, damn." It was said with too much bitterness to be sarcastic, and Jace knew that Jonathan had heard it because his eyes became softer.

"I think he was trying to get me – Sebastian – to hate you. He knew Sebastian could only feel negative emotions; jealousy, hate, anger, etc."

Jace didn't think he would ever get used to hearing Jonathan refer to his past self as Sebastian. Another reminder that the guy in front of him wasn't who he used to be.

"I guess it worked," Jace shrugged. "Sebastian seemed to absolutely hate me when I fought him. The only reason I'm even alive now is because he wanted to stay and talk."

An anguished expression crossed Jonathan's face. "I apologize for that."

Jace looked at him. "Why are you apologizing?"

"It was still me," Jonathan said, and now he was the bitter one. "No matter what anyone says – even though it was Valentine that made me into that _thing_ – it was _still me. _It was still my mind that made the decisions, still my hands that killed, still my mouth that smiled at the terror and shock that I had wreaked." His voice dropped to a whisper. "It was still me."

"No." Jace's voice was calm. "It was Lilith; and Valentine for experimenting with her blood. _He _did all this. It's _his _fault that you became Sebastian. I should know. I was raised by him. He gave me the same name he gave you; he trained me the same way he trained you; taught me the same things he taught you. In some ways, we're just like each other."

_"__To love is to destroy, and to be loved is to be the one destroyed," _Jonathan quoted, leaning his head back on the wall. "I remember."

"It was Clary who changed me," Jace continued. He didn't know himself what he was doing. He usually wasn't this forthcoming but something in him told him to keep going; to break through to the person who had been his brother in more ways than one. "Love isn't a weakness. It's a strength and it's the people who love us who make us stronger."

Jonathan was still leaning his head on the wall, his eyes closed. "I hope one day I can believe that."

"You will." The words came from the doorway.

Both boys turned in the direction of the voice. It was Clary.

Her face was calm, her voice absolutely sure; like she could see into the future and know what would happen to her brother.

Jace looked from one to another. Clary and Jonathan were so much more similar than he had initially realized. Jonathan may have gotten Valentine's white-blonde hair and tall frame but his eyes were Jocelyn's; vibrant, vivacious green. He had slender fingers and long eyelashes and without the persona of Sebastian, his face was softer, kinder.

Just like Clary.

Jace watched Clary lean up to whisper something to Jonathan, saw his face pale and experienced a moment of curiosity; what had Clary told him?

Clary folded her arms and stared at him, eyes stern. Jonathan looked at her for a minute, nodded and then walked out the door with a nod to Jace.

"What did you tell him?" Jace asked.

Clary looked at him, and he saw conflicted emotions play out in her green eyes. "I told him to go see his mother."

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><p>Jocelyn had lived with the guilt for eighteen years.<p>

Barely a day went by that she didn't think of her son, the boy who Valentine had stolen from her before she was even given a chance to get to know him.

She had tried so, so hard to keep from letting Clary see her pain. But on that one day every year, she let herself mourn for her lost child.

_"__Why are you crying, Mummy?" _

_Five year old Clary, her red hair braided into two plaits, came up to Jocelyn, looking worried. Jocelyn couldn't blame her; she had never cried in front of Clary before. _

_Just seeing Clary every day, she was reminded of Jonathan; he would have been six if he had lived. She knew it was for the best that he was dead – if he had lived, the damage he could have done to the world would have been astounding. She felt nothing for Valentine any longer; the moment he had turned their child into a monster, he had been dead to her. _

_What kind of father would do that to his own child? _

_Looking at her daughter now, she felt the tears spilling from her eyes again. She would never be able to tell Clary about the old Nephilim legends, never be able to show her around Alicante, never see her own daughter get her first rune. She would have to hide Clary from the Shadowhunter world for the rest of her life. _

_All because of Valentine. _

_She hugged Clary to her, sobbing into her soft red hair as Clary started to cry too, not knowing the reason but sobbing for whatever it was that had caused her strong, unbreakable mother to break down. _

"Mother?"

Jocelyn turned abruptly, not even realizing that her cheeks were wet until she saw a concerned expression cross her son's face. "Are you alright?"

"Jonathan?" she asked hoarsely, quickly wiping her cheeks with the back of her hand.

Jonathan wavered in the door, his expression conflicted. "I can go if you want…"

"No, no!" she said quickly. "Stay."

He walked in and she stood up from the chair to walk over to him. He looked nervous, unsure. It felt as if something hard and sharp had been driven into Jocelyn's chest. She had missed nearly seventeen years of his life. She didn't know anything about her son.

He might as well have been a stranger.

"Jonathan," she started, asking the question she desperately wanted to hear the answer to. "What did Valentine do to you?"

He flinched as if she had slapped him across the face and that's when she knew. Her horror and shock must have shown on her face because he reached out a hand as if to touch her shoulder and then seemed to think better of it, drawing his hand back.

"He beat you," she whispered. "Didn't he?"

Jonathan looked hesitant, and then he nodded. "He beat us both," he told her. "Jace and me. He said I – I should be stronger, I should be able to bear pain. He whipped me with demon metal."

Jocelyn's hand flew to her mouth. "Demon metal?" she whispered. "Is it – are the marks still there?"

He turned around and took off his shirt. Jocelyn stared at his back; it was criss-crossed with lash marks, and she couldn't begin to imagine how it must have hurt. "Oh Jonathan," she murmured, gently touching one of the scars. "I am so sorry."

Jonathan turned back to her. "No, Mom," he said gently. "Please don't apologize. It's not your fault."

"Valentine," Jocelyn said and her green eyes were dark with hatred. "He did this. I'm glad he's dead. I wish he burns in _hell_."

She was surprised by her own vehemence, but seeing the marks of violence on the gentle boy in front of her, it had risen inside her.

She rose up on her toes and kissed his forehead. She could feel her own tears falling from her eyes again, but this time they were tears of relief and joy. She may have missed seventeen years of his life, but he was still her son and she could already feel the strength of her affection for him.

Her son the way he should be, pure and untainted, a boy who was able to love and care and _feel_.

"I was so lonely," Jonathan said suddenly. "When I was Sebastian. Valentine didn't – he didn't love me. No one did. And I didn't know what love was or how to love someone, but I wanted to be loved. I think there was a small part of me that remained untouched by Lilith's blood, and that human part of me was you."

"I never realized," he continued. "Until I was rid of the demon blood. Until it was cleansed from my veins, I never realized how much it was weighing me down."

He looked at her and suddenly smiled, a joyful, happy smile that made him seem younger.

"I never felt so light."

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><p><em>Yay! Another chapter done! <em>

_I have plans for this story, so it won't be fluff all the time. Soon enough the real plot will develop and then there will be drama and adventure for anyone who's getting tired of seeing just Jonathan bond with people. _

_Oh, and just to clarify: this is FanFiction and Cassandra Clare wrote about Jonathan for, like, two pages. She gave very little clue as to what his personality is like, but I think he's kind and gentle, and he feels remorseful for his actions. _

_Just to make it clear – I might not capture Jonathan's personality perfectly and for that I apologize right now. I am writing him the way I think he would be. _

_Tell me what you thought about Jace and Jonathan and Jocelyn and if you liked this chapter or not. _

_Till next time! _


	4. Chapter 3

_I was reading the Infernal Devices, and I was sobbing and laughing and going on a rollercoaster of emotions all at the same time – is it just me, or did you all feel that way too? _

_Throughout Clockwork Prince I was like shipping Tessa and Jem so hard and then in Clockwork Princess I was shipping Tessa and Jem and Tessa and Will at the same time. _

_Both Jace and Will got laid in the last books – and they pick the absolute worst times EVER to do it. In a demon dimension with the fate of the world in your hands? Trapped in a room while a raving lunatic builds an army of clockwork machines that could kill you? Yep! This seems like the perfect time to get it on! _

_You Herondale boys really need to keep your hormones under control. _

_And now that that rant is over, I'm going to proceed with the story._

_Disclaimer: I do not own the Mortal Instruments._

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><p><em>"Heart beats fast, colors and promises. How to be brave, how can I love when I'm afraid to fall but watching you stand alone...All of my doubts, suddenly goes away somehow. One step closer... I<em>_ have died every day, waiting for you. Darling don't be afraid, I have loved you for a thousand years. I'll love you for a thousand more..." _

- _A Thousand Years, Christina Perri_

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><p><strong>Chapter Three<strong>

Clary could see the smoke from her window.

She wanted to turn away but something kept her compelled, watching it rise higher and higher into the blue sky.

They were burning Valentine's body.

Jace had asked her if she wanted to go; he hadn't seem surprised when she had shaken her head. Nodding, he had left to go to the funeral.

She didn't know how he could go. This was the man who had whipped him bloody for the first ten years of his life, who had instilled in him that love was a weakness.

She remembered Jace telling her that he had wanted to take a bath in pasta – and Valentine had given it to him. She remembered the far-away look in his eyes sometimes when he recalled Valentine.

Blood wasn't love. Valentine had been her father but she hadn't loved him. Sebastian had been her brother, but she hadn't loved him. Yet Jace, who hadn't even been related to Valentine, still loved him.

Love was a complicated thing, she decided.

How did you know that there was only one person right for you? How had she known that Jace was the only one for her – even when she had thought they were siblings?

Dating Simon, kissing him, being his girlfriend – it hadn't felt wrong, exactly, but it hadn't been just right either. With Jace on the other hand, it had felt just like what she needed, like a breath of air after being trapped in an airless room for a long time.

"What are you thinking about?"

Clary looked around; it was Simon. She hadn't been able to have a real talk with him over the past few days; something or the other had always claimed her attention – re-telling her story again and again, standing for trial in front of all Shadowhunters….

The trial had been the day after Jonathan's return.

_"__Jonathan Morgenstern. Step forward and take the Mortal Sword." _

_Jonathan's face was set as his fingers closed around the hilt of the sword. There was a brief flash of pain on his face but it vanished as quickly as it had come and his mouth returned to the firm line it had been in before. _

_Clary cringed, knowing how it felt to hold the Mortal Sword. You couldn't lie but even if you wanted to tell the truth, it was agony – like hooks digging into your skin that dragged the truth out of you. _

_"__Jonathan, who is on the stage with you today?" Jia Penhallow asked, her voice loud and firm. _

_"__You, the Consul. The Inquisitor. My family – my mother Jocelyn Fairchild and my sister Clarissa Morgenstern." _

_"__Tell us how you – Sebastian," Jia corrected herself, "took down the wards of Alicante." _

_"__Sebastian used demon blood to take down the wards," Jonathan answered. "When my mother was pregnant with me, Valentine mixed powdered demon blood into her food. Because of it, Sebastian was born with demon blood in his veins."_

_Murmurs broke out among the Shadowhunters like little hissing fires. Valentine had poisoned his son with demon blood? _

_"__As he was a Shadowhunter, he could gain access to Alicante whenever he wanted it. He used his own blood to take down the demon towers." _

_Jia exchanged a look with Maryse Lightwood. "Tell us what you remember of the night of the Mortal War." _

_Jonathan gritted his teeth. "Valentine summoned me to the manor. He told me that the Shadowhunters were not going to surrender. He said that Clary had come up with a rune to ensure that Shadowhunters could draw on the strength of Downworlders. He was furious." _

_"__He told me to stay behind, to open the gates once it was midnight and let the demons in to do battle on Brocelind Plain. He was going to Lake Lyn, to use the Mortal Instruments and summon Raziel." _

_Only the Council had known about the summoning of Raziel up till that point. The Shadowhunters started to talk among themselves, shooting glances at Clary and Jonathan. _

_"__I – Sebastian – he knew Jace was there. But before he killed him, he wanted Jace to see the power Valentine wielded over the demons because of the Mortal Sword. He kept him alive to taunt him before he died." _

_"__And what did Valentine want with the Angel Raziel?" Jia demanded. _

_Jonathan fingers clasped the sword hilt tighter. He was clearly in pain, Clary could see, and she wasn't sure she would be able to stand it much longer. Her hands were already balled into fists. _

_Jonathan took a deep, shaky breath before responding. "The Angel is compelled to grant a favor asked by one wielding the Mortal Instruments. Valentine was going to ask the Angel to strip the powers of all those who hadn't drunk from the Mortal Cup – who weren't his followers. And since they would still bear Marks, they would become Forsaken, easy prey for demons." _

_Jocelyn's hand flew to her mouth, her eyes wide. Clary felt sick. _

_"__Jace taunted Sebastian. He goaded him into untying his hands and letting him fight. He knew it was the only way that he had a chance of surviving. They fought." _

_Jonathan's face was contorted in pain, his features twisted into a grimace. "Sebastian overpowered Jace. He was about to kill him when Isabelle arrived, and she cut off his hand with her whip." _

_Clary felt a wave of admiration for the girl. _

_"__In the end, Jace managed to kill Sebastian, and I – I remember feeling like all sense was gone, like I was floating in a sea of black –"_

_Jonathan gasped and sank to his knees, his hands trembling. It was clear that the strain of holding the Mortal Sword for so long had drained him. Clary was sprinting across to her brother before she knew what she was doing, feeling a wave of anger against the Clave. He would have told them the truth. They didn't have to torture him! _

_She knelt down beside him and grasped the hilt of the sword, one hand over Jonathan's, reassuring him. "He can't tell you anything else," she said strongly, her conviction clear in her voice. "I was the one who saw Valentine summon Raziel. He needed my blood for the ritual. When he was chanting, I changed some of the runes – changed his name to my own so that the Mortal Instruments afforded him no protection." _

_The Council room was quiet, everyone hanging on to her every word. Clary had already shown the Clave what had happened, but she knew the other Shadowhunters needed to know the truth of what had happened that night. _

_"__When Raziel appeared, he knew what Valentine had done."_

_There was a collective gasp from the room. "You met the Angel Raziel?" Jia asked, shocked. She hadn't been there when Clary had shown the Clave what had happened on the shores of Lake Lyn. _

_Clary nodded. "The Angel knew what Valentine wanted was for his own glory, and so he killed him. He told me the battle on Brocelind Plain was ending and asked me what I wanted. I told him I wanted my brother back," Clary swallowed, feeling the sword pulling the truth out of her. _

_"__He told me to close my eyes. And when I opened them, I saw Jonathan kneeling beside me." _

_Jia turned her attention to Jonathan. "And what about you, Jonathan?"_

_"__I felt a tug," Jonathan said, "as if something was pulling me back to the world of the living. I heard Clary say my name and then I was beside her, kneeling in the sand." _

_"__So you are purged of the demon blood?" Robert Lightwood questioned. _

_"__Yes," Clary said firmly. "I asked the Angel himself to do it. If you question that Jonathan's blood is still not pure, then you are questioning the power of the Angel." _

_ "__Very well," Jia said, sighing. "Jonathan and Clarissa Morgenstern, you may release the Mortal Sword."_

"Hello? Earth to Clary?" Simon snapped his fingers in front of Clary's face, effectively bringing her back from her memories.

She batted his hand away. "Quit it, Simon."

"So you're alive then," he teased. "I was afraid you'd turned to stone there for a second. What were you thinking about?"

She shoulder-bumped him, smiling. No matter what happened in her life, she knew she could always count on Simon being there for her, steady and reliable like a rock of support. "Valentine," she said, gesturing towards the window and the spiral of smoke, getting ever higher.

There was no need for her to say anymore – Simon understood what she was feeling. That was the plus point of being friends with someone for more than a decade; they knew exactly what you were trying to say without you having to actually say it.

He wrapped an arm around her shoulders and they sat there together, neither of them saying a word.

Jocelyn and Luke were up at the Accords Hall – Clary wasn't quite sure for what. Alec and Isabelle and Jace had all gone to the funerals of the dead Shadowhunters.

Clary yearned to speak to Jace. Now that they both knew they weren't siblings, they could be…what? In a relationship?

What if Jace didn't want her anymore? What if he had loved her purely because she was the proverbial forbidden apple?

Simon nudged her. "Snap out of it, Fray."

"Out of what?"

"Out of your Jace daydreams."

"How did you know I was thinking about Jace?" Clary demanded.

Simon scoffed. "Please. I'm your best friend. And it's written all over your face. Give me some credit."

Simon made what was clearly supposed to be a soppy face. "Oh Jace," he cried dramatically. "I love you!"

Clary smacked him on the arm. "I do _not_ look like that," she protested. "And I certainly don't sound like that."

"Hate to break it to you," Simon shrugged, "but you do."

"And what about your love life?" Clary demanded. "Isabelle and Maia both like you, you know."

Simon suddenly looked horrified. "They do?"

Clary shook her head. "Boys."

"But-but what should I do?" Simon demanded.

"Well, do you like them back?"

Simon contemplated this. "Maybe?"

Clary made an exasperated noise. "Simon!"

"Look, I don't know okay?" Simon defended himself. "They're both hot and…way out of my league. And sometimes they get together and whisper and _stare_ at me. I have no idea what it's about."

"Sure you don't," Clary grinned. "Poor you, you have two cute girls vying for your love. Your life is hard."

"Fine. You tell me which one to choose then."

Clary held up her hands. "No way. That's totally on you." Then she lowered her voice. "Look, you can date whoever you want and I will _totally _support you. I am all about support. Support is my middle name."

"So _that's_ why you never told me your middle name. I figured it was something embarrassing."

Clary ignored this. "But just promise me something, okay? I know how girls get. I know how they hate their boyfriends having a best friend who's a girl. Just promise me you won't cut me out of your life totally. That we can still hang out sometimes."

"Sometimes?" Simon shook his head. "Clary, you're crazy."

Her heart sank. "You mean …"

"I mean that I would never date a girl who insisted that I cut you out of my life. It's non-negotiable. You want a piece of all this fabulousness?" He gestured at himself. "Well, my best friend comes along with it. I wouldn't cut you out of my life, Clary, any more than I would cut off my right hand and give it to someone as a Valentine's Day gift."

"Gross," said Clary. "Must you?"

He grinned. "I must."

Just then, they both heard the sounds of someone coming up the stairs and fell silent.

It was Jonathan.

"So _this _is where you guys are," he sighed in relief. "Mom's been looking for you, Clary."

"For me?" Clary jumped off the bed, making her way to the door. "Why?"

Jonathan shrugged. "I don't know. I think it's something about the celebration. Since Clary's a hero of the Mortal War – "

"Wait, what?" Clary interrupted.

Her brother looked at her in surprise. "You don't know? Clary, you're the one who came up with the Alliance Rune – you don't know how many lives you saved. And summoning the Angel Raziel – "

"Technically, that was Valentine."

"Yes, but you've actually met the Angel and lived to talk about it. You're the first person to have done that since Jonathan Shadowhunter."

Clary looked taken aback. "I didn't realize."

"Is she the only one?" Simon asked.

"No, Jace and Isabelle too."

"Jace and Isabelle?" Simon asked, surprised. "Why?"

Jonathan looked uncomfortable. "Because they're the ones who killed Sebastian."

"I thought that was Jace?" Simon demanded.

"Jace was the one who pierced his heart but if it hadn't been for Isabelle he would definitely have been killed. Isabelle interrupted just in time, and Jace killed him while he was distracted with her."

"Oh." Simon looked at a loss as to what to say. "Well, lucky Isabelle was there."

"Just a piece of advice, Simon," Jonathan grinned. "Whatever you do, don't get Isabelle pissed at you because I've learned first-hand that she is _deadly _with that whip."

* * *

><p>"This tickles," Clary complained as Isabelle arranged her red hair over her shoulders before stepping back to appraise her. "There," she said, "you look fantastic."<p>

Clary sighed but decided not to say anything as Isabelle turned to the mirror and slid a barrette into her dark hair, pinning the front strands back. "Ready to go?"

"Sure," Clary shrugged and both girls headed downstairs.

Jocelyn was talking to Maryse Lightwood, both of them smiling as they chatted. Clary reflected on how nice it was to see everyone happy for once instead of constantly having a worried frown on their face.

Jonathan was saying something to Alec, both boys dressed in jeans and sweaters. Alec looked happier too, as if a heavy weight had been lifted off his shoulders. Clary wondered idly whether he and Magnus had DTRed yet.

"Clary!" her mother exclaimed, noticing her for the first time. "Darling, you look beautiful."

"Thanks," Clary murmured, still tugging a little self-consciously at the hem of the dress, not used to having her bare legs exposed.

"Congratulations Clary," Maryse smiled at her. "The Council couldn't have made a better choice, I must say."

"About?" Clary asked, curious.

"You don't know?" her mother questioned. "I asked Jonathan to tell you – "

"She didn't give me a chance to," her brother protested, appearing at her side as if by magic. "Before I could even get it out, she was already off."

Jocelyn sighed in pretend exasperation, shaking her head at both of her children. "Well Clary, the Council wants to know if you'll be willing to draw the symbol for the New Council."

Isabelle looked impressed. "That's a huge honour," she told Clary. "They say that Jonathan Shadowhunter was the only one to come up with a symbol for the Council before – and that's the one they've kept for a thousand years."

"Sure," Clary agreed. "I'd be happy to."

* * *

><p><em>"<em>_The Accords Hall steps. Go."_

Clary could see a familiar dark outline seated in the shadow of a pillar, his golden hair bright even from a distance. Her heart quickened.

Jace.

It was the first time she had ever really been alone with him. She stopped a little distance away, unsure what to say.

As if sensing her there, Jace looked up. He was holding something balanced in his lap, she saw, a silvery box. He looked tired. There were shadows under his eyes, and his pale gold hair was untidy. His eyes widened. "Clary?"

"Who else would it be?"

He didn't smile. "You don't look like you."

"It's the dress." She smoothed her hands down the material self-consciously. "I don't usually wear things this … pretty."

"You always look beautiful," he said, and she remembered the first time he'd called her beautiful, in the greenhouse at the Institute. He hadn't said it like it was a compliment, but just as if it were an accepted fact, like the fact that she had red hair and liked to draw. "But you look—distant. Like I couldn't touch you."

She came over then and sat down next to him on the wide top step. The stone was cold through the material of her dress. She held her hand out to him; it was shaking slightly, just enough to be visible. "Touch me," she said. "If you want to."

He took her hand and laid it against his cheek for a moment. Then he set it back down in her lap, but didn't remove his hand from hers.

"What's in the box?" she asked. He was still clutching the silver rectangle tightly in one hand. It was an expensive-looking object, delicately carved with a pattern of birds. "I went to Amatis's earlier today, looking for you," he said. "But you weren't there. So

I talked to Amatis. She gave me this." He indicated the box. "It belonged to my father."

For a minute, she thought he was talking about Valentine, before she realized that he was referring to his biological father. "Of course," she said. "Amatis was married to Stephen Herondale."

"I've been going through it," he said. "Reading the letters, the journal pages. I thought if I did that, I might feel some sort of connection to him. Something that would leap off the pages at me, saying, _Yes, this is your father_. But I don't feel anything. Just bits of paper. Anyone could have written these things."

"Jace," she said softly.

"And that's another thing," he said. "I don't have a name anymore, do I? I'm not Jonathan Christopher—that was someone else. But it's the name I'm used to."

"Who came up with Jace as a nickname? Did you come up with it yourself?"

Jace shook his head. "No. Valentine always called me Jonathan. And that's what they called me when I first got to the Institute. I was never supposed to think my name was Jonathan Christopher, you know—that was an accident. I got the name out of my father's journal, but it wasn't me he was talking about. It wasn't my progress he was recording. It was Seb—It was Jonathan's. So the first time I ever told Maryse that my middle name was Christopher, she told herself that she'd just remembered wrong, and Christopher had been Michael's son's middle name. But that was when she started calling me Jace: It was like she wanted to give me a new name, something that belonged to her, to my life in New York. And I liked it. I'd never liked Jonathan." He turned the box over in his hands. "I wonder if maybe Maryse knew, or guessed, but just didn't want to know. She loved me … and she didn't want to believe it."

"Which is why she was so upset when she found out you were Valentine's son," said Clary. "Because she thought she ought to have known. I think she kind of did know, but she just pushed it to the back of her mind because we never do want to believe things like that about people we love. But Jace she was right about you – about who you really are. And you do have a name. Your name is Jace. Valentine didn't give that name to you. Maryse did. The only thing that makes a name important is that it's given to you by someone who loves you."

"Jace what?" he said. "Jace Herondale?"

"Oh, please," she said. "You're Jace Lightwood. You know that."

He still looked a little lost, like a confused little boy in the street searching for his parents.

"Maybe you're a different person than you thought you were," she went on, hoping against hope that he understood what she meant. "But no one becomes a totally different person overnight. Finding out that Stephen was your biological father isn't going to automatically make you love him. And you don't have to. Valentine wasn't your real father, but not because you don't have his blood in your veins. He wasn't your real father because he didn't act like a father. He didn't take care of you. It's always been the Lightwoods who have taken care of you. They're your family. Just like Mom and Luke are mine."

She bit her lip, suddenly feeling like a nag. "I'm sorry," she said. "You probably came out here to be alone and here I am coming and lecturing you – "

"You're right," he interrupted her, raising his eyes to hers.

Clary felt like someone punched her in the gut. She stood up, forgetting to hold her dress up, and nearly stepped on the hem.

"Clary!" Setting the box down, Jace scrambled to his feet. "Clary, wait. That wasn't what I meant. I didn't mean I wanted to be alone. I meant you were right about Valentine—about the Lightwoods—"

She turned and looked at him. He was standing half in and half out of the shadows, the bright, coloured lights of the party below casting strange patterns across his skin. She remembered the first time she had seen him and how the image of a lion had sprung to her mind – beautiful and deadly, able to kill you with a single blow but with a certain grace while doing it.

But that was gone now. That hard, defensive casing he wore like armour was gone, and he wore his injuries instead, visibly and proudly. He hadn't even used his stele to take away the bruises on his face, along the line of his jaw, at his throat where the skin showed above the collar of his shirt. But he looked beautiful to her still, more than before, because now he seemed human—human, and real.

"You know," she said, "I was wondering if maybe you weren't that interested anymore. Now that it isn't forbidden – that you could be with me if you wanted to." She shivered a little in the flimsy dress, gripping her elbows with her hands. "Is that true? Are you not… interested?"

"Interested? As if you were a—a book, or a piece of news? No, I'm not interested. I'm—" He broke off, groping for the word the way someone might grope for a light switch in the dark. "God, Clary – "

"What?"

He reached out and gripped her hands, his golden eyes searching her own green ones, as if looking for something. "Do you remember what I said to you before? About feeling like the fact that you were my sister was a sort of cosmic joke on me? On both of us?"

"I remember."

"I never really believed it," he said. "I mean, in a way I thought it was true – but I never thought that the one person I wanted could be the one person I couldn't have. Because I never felt about you the way brothers are supposed to feel about their sisters."

Clary was holding her breath, hanging onto his every word.

"But at the same time, I felt like there was something _right_ about us – something that I hadn't felt with anyone else. As if you were a part of me, like my heart or my soul. I've always felt that."

Seeing her puzzled expression, he broke off with an impatient noise. "I'm not saying this right. Clary, I hated every second that I thought you were my sister. I hated every moment that I thought what I felt for you meant there was something wrong with me. But—"

"But what?" Clary's heart was beating so hard it was making her feel more than a little dizzy.

"I could see the delight Valentine took in the way I felt about you. The way you felt about me. He used it as a weapon against us. And that made me hate him. More than anything else he'd ever done to me, that made me hate him, and it made me turn against him, and maybe that's what I needed to do. Because there were times I didn't know if I wanted to follow him or not. It was a hard choice—harder than I like to remember." His voice sounded tight.

"I asked you if I had a choice once," Clary reminded him. "And you said, 'We always have choices.' You chose against Valentine. In the end that was the choice you made, and it doesn't matter how hard it was to make it. It matters that you did."

"I know," Jace said. "I'm just saying that I think I chose the way I did in part because of you. Since I've met you, everything I've done has been in part because of you. I can't untie myself from you, Clary—not my heart or my blood or my mind or any other part of me. And I don't want to."

"You don't?" she whispered.

He took a step towards her, so close that they were pressed right up against each other, his hands forming manacles around her wrists. And yet, she found that she didn't want him to step away, to let her go.

"No. I always thought love made you weak, that it made you a bad Shadowhunter. _To love is to destroy. _I believed what Valentine taught me, because at the time I didn't know anything else. I used to think not caring made me a good fighter – and then I met you."

His voice was low now, and his fingers slipped into hers. Their gazes locked and held.

"You had never been trained. You weren't a fighter. You didn't even know how to use a stele, or a seraph blade. And I saw how you walked into that vampire hotel to save Simon, how you would have done anything to find your mother – because you loved them. Shadowhunters with a decade of experience wouldn't have done that."

"And I realized that I was wrong. Love didn't make you weak; it made you stronger than anyone I'd ever met. And I think that, Clary, was when I started to fall in love with _you_."

He was speaking faster now, his gaze desperately searching her face for some sign, any sign of what she was feeling. Clary's heart was beating like a drum.

"Everything I've done since I met you, Clary, I've only been able to do because of you. You've influenced every decision I made. By all means, Sebastian should have killed me. He was the better fighter, the one with more training. He nearly did. But the only reason I was able to get up and fight back was because I thought of you – and I saw you standing there in front of me with your bright green eyes, willing me to stand up and fight – and I did because I wanted to live, just so I could see those eyes of yours again – "

One of his hands gently loosened from hers and cupped her face, his thumb stroking her cheekbone.

"And hear you speak, even if it was just for a moment more. I love you, Clary. I love you more than I've ever loved anything in my life and now you're standing here asking me if I still _want _you, as if I haven't wanted you from the first moment I saw you. I've always belonged to you. If you still want _me_, that is."

She stood frozen for a minute, unable to react – and then her lips crashed against his and they were kissing. His arms pulled her tighter against him and hers locked around his neck, pulling him down to her, and the feel of his mouth against hers was electric and fizzing with something she couldn't name, something that felt full of heat and passion and like a deep breath of air after being underwater for a long time –

Jace broke away, and she looked up at him; his eyes had a light in them again, now with a wicked sparkle. "You know if it's the lack of forbidden you're worried about," he whispered, "you could still forbid me to do things."

"Like what?" she asked.

His mouth brushed against hers again. "Like this."

She smiled against his lips. "Somehow, I don't think that will be a problem."

* * *

><p><em>So I gave you a pretty long chapter – I changed the last few pages somewhat from City of Glass, and Jace's speech to Clary because I didn't want to seem like a huge plagiarizer. However, majority of their speeches are from Cassandra Clare, as I'm sure you will recognize so please don't sue me –I'm just a fangirl enjoying a Clace moment. <em>

_Review, please – it would really make my day :)_

_Till next time! _


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